diff options
| -rwxr-xr-x | examples/classification.scm | 128 |
1 files changed, 59 insertions, 69 deletions
diff --git a/examples/classification.scm b/examples/classification.scm index 27c8d98..4af9a3c 100755 --- a/examples/classification.scm +++ b/examples/classification.scm @@ -21,41 +21,24 @@ (gnc:resource_classification_scheme skos:prefLabel "GeneNetwork Resource Classification Scheme") (gnc:resource_classification_scheme skos:definition "A hierarchical classification scheme for organizing GeneNetwork resources by dataset type, resource set (inbredset group), or species.") (gnc:resource_classification_scheme xkos:numberOfLevels "4") - (gnc:resource_classification_scheme xkos:levels gnc:dataset_type) - (gnc:resource_classification_scheme xkos:levels gnc:set) + (gnc:resource_classification_scheme xkos:levels gnc:taxonomic_family) (gnc:resource_classification_scheme xkos:levels gnc:species) - (gnc:resource_classification_scheme xkos:levels gnc:family) - (gnc:dataset_type a xkos:ClassificationLevel) - (gnc:dataset_type skos:inScheme gnc:resource_classification_scheme) - (gnc:dataset_type skos:prefLabel "Dataset Type") - (gnc:dataset_type skos:definition "Classification level describing the biological or experimental nature of a dataset. A dataset can either be a probeSet, a genotype or a phenotype.") - (gnc:dataset_type xkos:depth "1") - (gnc:dataset_type xkos:nextLevel gnc:set) - (gnc:dataset_type skos:member gnc:probeset) - (gnc:dataset_type skos:member gnc:genotype) - (gnc:dataset_type skos:member gnc:phenotype) - (gnc:probeset a skos:Concept) - (gnc:probeset skos:inScheme gnc:dataset_type) - (gnc:probeset skos:prefLabel "Transcriptomic Datasets") - (gnc:probeset skos:altLabel "ProbeSet") - (gnc:probeset skos:definition "A category representing microarray or sequencing probe sets that measure gene expression or other molecular traits.") - (gnc:probeset skos:note "Individual probe sets are too numerous to list explicitly in this ontology but are available through the GeneNetwork API.") - (gnc:genotype a skos:Concept) - (gnc:genotype skos:inScheme gnc:dataset_type) - (gnc:genotype skos:prefLabel "Genotype Datasets") - (gnc:genotype skos:altLabel "Genotype") - (gnc:genotype skos:definition "A category representing genetic marker or variant datasets used for genetic mapping.") - (gnc:phenotype a skos:Concept) - (gnc:phenotype skos:inScheme gnc:dataset_type) - (gnc:phenotype skos:prefLabel "Phenotype Datasets") - (gnc:phenotype skos:altLabel "Phenotype") - (gnc:phenotype skos:definition "A category representing measured traits or phenotypes for genetic analysis.") + (gnc:resource_classification_scheme xkos:levels gnc:set) + (gnc:resource_classification_scheme xkos:levels gnc:population_category) + (gnc:population_category a xkos:ClassificationLevel) + (gnc:population_category skos:inScheme gnc:resource_classification_scheme) + (gnc:population_category xkos:nextLevel gnc:set) + (gnc:population_category skos:prefLabel "Species") + (gnc:population_category rdfs:label "Population Category") + (gnc:population_category xkos:depth "4") + (gnt:population_category skos:definition "Classification of genetic populations by breeding design and data aggregation.") (gnc:species a xkos:ClassificationLevel) (gnc:species skos:inScheme gnc:resource_classification_scheme) - (gnc:species xkos:previousLevel gnc:set) + (gnc:species xkos:previousLevel gnc:taxonomic_family) + (gnc:species xkos:nextLevel gnc:set) (gnc:species skos:prefLabel "Species") (gnc:species skos:definition "A classification level that that associates a given resource to a species in GeneNetwork.") - (gnc:species xkos:depth "3")) + (gnc:species xkos:depth "2")) (triples "gnc:species" (set skos:member (string->identifier "" (remap-species-identifiers (field Species Fullname)))))) @@ -66,11 +49,11 @@ (schema-triples (gnc:set a xkos:ClassificationLevel) (gnc:set skos:inScheme gnc:resource_classification_scheme) - (gnc:set xkos:nextLevel gnc:species) - (gnc:set xkos:previousLevel gnc:dataset_type) + (gnc:set xkos:nextLevel gnc:population_category) + (gnc:set xkos:previousLevel gnc:species) (gnc:set skos:prefLabel "InbredSet Group") (gnc:set skos:definition "A category representing groups of genetically related strains or individuals (inbred sets, recombinant inbred lines, etc.).") - (gnc:set xkos:depth "2")) + (gnc:set xkos:depth "3")) (triples "gnc:set" (set skos:member (string->identifier @@ -81,11 +64,11 @@ (schema-triples (gnt:has_uniprot_taxon_id a owl:ObjectProperty) (gnt:has_uniprot_taxon_id rdfs:label "has uniprot taxonomic id") - (gnt:has_family a owl:ObjectProperty) - (gnt:has_family rdfs:label "has family") - (gnt:has_family skos:definition "Links a species to its taxonomic family") - (gnt:has_family schema:domainIncludes gnc:species) - (gnt:has_family schema:domainIncludes gnc:set) + (gnt:has_taxonomic_family a owl:ObjectProperty) + (gnt:has_taxonomic_family rdfs:label "has family") + (gnt:has_taxonomic_family skos:definition "Links a species to its taxonomic family") + (gnt:has_taxonomic_family schema:domainIncludes gnc:species) + (gnt:has_taxonomic_family schema:domainIncludes gnc:set) (gnt:short_name a owl:DatatypeProperty) (gnt:short_name rdfs:label "has short name") (gnt:short_name rdfs:domain gnc:species) @@ -101,7 +84,7 @@ (set skos:prefLabel (field Species MenuName)) (set skos:altLabel (field Species SpeciesName)) (set gnt:short_name (field Species Name)) - (set gnt:has_family (string->identifier "family" (field Species Family) #:separator "_")) + (set gnt:has_taxonomic_family (string->identifier "family" (field Species Family) #:separator "_")) (set gnt:has_uniprot_taxon_id (ontology 'taxon: (field Species TaxonomyId))))) @@ -125,12 +108,12 @@ (tables (Species) "GROUP BY FAMILY") (schema-triples - (gnc:family a xkos:ClassificationLevel) - (gnc:family skos:inScheme gnc:resource_classification_scheme) - (gnc:family skos:prefLabel "Family") - (gnc:family skos:definition "An organizational classification level used in GeneNetwork to group resources into families.") - (gnc:family xkos:depth "4") - (gnc:family xkos:previousLevel gnc:species) + (gnc:taxonomic_family a xkos:ClassificationLevel) + (gnc:taxonomic_family skos:inScheme gnc:resource_classification_scheme) + (gnc:taxonomic_family skos:prefLabel "Family") + (gnc:taxonomic_family skos:definition "An organizational classification level used in GeneNetwork to group resources into families.") + (gnc:taxonomic_family xkos:depth "1") + (gnc:taxonomic_family xkos:nextLevel gnc:species) (gnt:has_family_order_id a owl:DatatypeProperty) (gnt:has_family_order_id rdfs:range xsd:integer)) (triples (string->identifier "family" (field Species Family) #:separator "_") @@ -167,8 +150,6 @@ (gnt:has_set_code skos:definition "Provides a unique identifier code for a resource set.") (gnt:has_set_code rdfs:domain gnc:set) (gnt:has_set_code rdfs:range xsd:string) - ;; Already defined as an owl prop in species - (gnt:has_family rdfs:domain gnc:set) (gnt:uses_mapping_method a owl:ObjectProperty) (gnt:uses_mapping_method rdfs:label "mapping method") (gnt:uses_mapping_method rdfs:domain gnc:set) @@ -193,39 +174,48 @@ (set gnt:has_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))))) -(define-transformer inbredset-families* +(define-transformer inbredset-population* (tables (InbredSet) "WHERE Family IS NOT NULL") + (schema-triples + (gnt:has_population_category rdfs:domain gnc:set) + (gnt:has_population_category a owl:ObjectProperty) + (gnt:has_population_category rdfs:comment "This group belongs to this population category.") + (gnt:has_population_category rdfs:label "belongs to population category.")) (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") - (set gnt:has_family (string->identifier "family" (field InbredSet Family) #:separator "_")))) + (set gnt:has_population_category + (string->identifier "population" (field InbredSet Family) #:separator "_")))) -(define-transformer inbredset-families-list +(define-transformer inbredset-population-list (tables (InbredSet) "WHERE Family IS NOT NULL GROUP BY Family") - (triples (string->identifier "family" (field InbredSet Family) #:separator "_") - (set rdf:type 'gnc:family) + (schema-triples + (gnc:reference_population a skos:Concept) + (gnc:reference_population a gnc:PopulationCategory) + (gnc:reference_population skos:inScheme gnc:population_category_scheme) + (gnc:reference_population skos:prefLabel "Reference population") + (gnc:reference_population skos:definition "A genetic population")) + (triples (string->identifier "population" (field InbredSet Family) #:separator "_") + (set rdf:type 'gnc:reference_population) (set rdfs:label (field InbredSet Family)) - (set gnt:has_family_order_id + (set skos:member 'gnc:population_category) + (set gnt:has_population_order_id (annotate-field (field InbredSet FamilyOrder) '^^xsd:integer)))) -(define-transformer inbredset-families-fanout +(define-transformer inbredset-population-fanout (tables (InbredSet) "WHERE Family IS NOT NULL") - (triples (string->identifier "family" (field InbredSet Family) #:separator "_") + (triples (string->identifier "population" (field InbredSet Family) #:separator "_") (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) -(define-transformer family-category-inbredset +(define-transformer population-category-inbredset (tables (InbredSet) "WHERE public > 0 GROUP BY Family") - (schema-triples - (gnt:assigned_strain rdfs:domain gnc:set) - (gnt:assigned_strain a owl:ObjectProperty) - (gnt:assigned_strain rdfs:label "These families have been assigned to these strains")) - (triples "gnc:family" - (set gnt:assigned_strain - (string->identifier "family" (field InbredSet Family) #:separator "_")))) + (triples "gnc:population_category" + (set gnt:has_population_category + (string->identifier "population" (field InbredSet Family) #:separator "_")))) (define-transformer family-category-species (tables (Species) @@ -234,8 +224,8 @@ (gnt:assigned_species rdfs:domain gnc:set) (gnt:assigned_species a owl:ObjectProperty) (gnt:assigned_species rdfs:label "These families have been assigned to these species")) - (triples "gnc:family" - (set gnt:assigned_species + (triples "gnc:taxonomic_family" + (set gnt:has_taxonomic_family (string->identifier "family" (field Species Family) #:separator "_")))) @@ -276,12 +266,12 @@ species species-fan-out inbred-set - inbredset-families* + inbredset-population* species-families-list species-families-fanout - inbredset-families-list - inbredset-families-fanout - family-category-inbredset + inbredset-population-list + inbredset-population-fanout + population-category-inbredset family-category-species)) (outputs `(#:documentation ,documentation |